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This recognition is elicited by the interaction between T\u2010Cell Receptors (TCRs) and epitopes, which consist of antigenic peptides displayed on major histocompatibility complex molecules. TCR\u2010epitope interactions are characterized by high diversity in TCR and epitope sequences and high structural flexibility in TCR loops. As a result, deciphering the rules of TCR\u2010epitope recognition specificity and accurately predicting these interactions remains challenging. Here, we review the different strategies developed to predict TCR\u2010epitope recognition, classify the principal computational frameworks, examine the data modalities on which they depend and discuss their current limitations. We then synthesize key conceptual insights that have emerged from recent research and outline how these lessons should inform the design of future experiments and next\u2010generation computational tools.<\/jats:p>","DOI":"10.1111\/imr.70140","type":"journal-article","created":{"date-parts":[[2026,7,10]],"date-time":"2026-07-10T06:59:03Z","timestamp":1783666743000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Modeling\n                    <scp>TCR<\/scp>\n                    \u2010Epitope Recognition Specificity: What We Should Learn to Succeed"],"prefix":"10.1111","volume":"340","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3952-0930","authenticated-orcid":false,"given":"David","family":"Gfeller","sequence":"first","affiliation":[{"name":"Department of Fundamental Oncology University of Lausanne  Lausanne Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB)  Lausanne Switzerland"},{"name":"Agora Cancer Research Centre  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Racle","sequence":"additional","affiliation":[{"name":"Department of Fundamental Oncology University of Lausanne  Lausanne Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB)  Lausanne Switzerland"},{"name":"Agora Cancer Research Centre  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rita Ann","family":"Roessner","sequence":"additional","affiliation":[{"name":"Department of Fundamental Oncology University of Lausanne  Lausanne Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB)  Lausanne Switzerland"},{"name":"Agora Cancer Research Centre  Lausanne Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,7,9]]},"reference":[{"key":"e_1_2_11_2_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1003466"},{"key":"e_1_2_11_3_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1606774"},{"key":"e_1_2_11_4_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010021\u201003752\u20104"},{"key":"e_1_2_11_5_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.271.5256.1734"},{"key":"e_1_2_11_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22991"},{"key":"e_1_2_11_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature23003"},{"key":"e_1_2_11_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010024\u201008507\u20105"},{"key":"e_1_2_11_9_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1251102"},{"key":"e_1_2_11_10_1","doi-asserted-by":"publisher","DOI":"10.1158\/1078-0432.CCR-11-0116"},{"key":"e_1_2_11_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140\u20106736(24)00319\u20102"},{"key":"e_1_2_11_12_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2005.07.015"},{"key":"e_1_2_11_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/nri1977"},{"key":"e_1_2_11_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature22383"},{"key":"e_1_2_11_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/imr.13439"},{"key":"e_1_2_11_16_1","doi-asserted-by":"crossref","unstructured":"Y.Liu G.Croce D.Tadros et\u00a0al. \u201cKey Determinants of T Cell Epitope Recognition Revealed by TCR Specificity Profiles \u201dbioRxiv (2025) https:\/\/doi.org\/10.1101\/2025.11.17.688817.","DOI":"10.1101\/2025.11.17.688817"},{"key":"e_1_2_11_17_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586\u2010024\u201007487\u2010w"},{"key":"e_1_2_11_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkad356"},{"key":"e_1_2_11_19_1","doi-asserted-by":"crossref","unstructured":"A.Ascunce\u2010Par\u00eds R.Farriol\u2010Duran M.Romero\u2010Durana A.Valencia andV.Guallar \u201cA Unified Framework for TCR\u2010pMHC Structural Model Assessment \u201dbioRxiv (2025) https:\/\/doi.org\/10.1101\/2025.10.09.681411.","DOI":"10.1101\/2025.10.09.681411"},{"key":"e_1_2_11_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41592\u2010024\u201002240\u20107"},{"key":"e_1_2_11_21_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.286.5441.958"},{"key":"e_1_2_11_22_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1212755109"},{"key":"e_1_2_11_23_1","doi-asserted-by":"crossref","unstructured":"T.MoraandA. 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